Is SETBP1 p.Phe362fs (c.1082_1083dup) pathogenic?

SETBP1 p.Phe362fs (c.10821083dup) is classified Pathogenic in SETBP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-03-21). Absent from gnomAD; Associated with intellectual disability, autosomal dominant 29.

What condition is associated with SETBP1 p.Phe362fs (c.1082_1083dup)?

SETBP1 p.Phe362fs (c.1082_1083dup) is associated with intellectual disability, autosomal dominant 29 (ClinVar).

How common is SETBP1 p.Phe362fs (c.1082_1083dup) in the general population?

SETBP1 p.Phe362fs (c.1082_1083dup) is absent from gnomAD (gnomAD).

How is Non-specific syndromic intellectual disability inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

SETBP1 p.Phe362fs

c.1082_1083dup · rs2071314703 · VCV976037

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

intellectual disability, autosomal dominant 29

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 4 of 6
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 1.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SETBP1
Protein: p.Phe362fs
Coding: c.1082_1083dup
MANE Select: NM_015559
dbSNP: rs2071314703
Type: Duplication
Location: chr18:44950421 (GRCh38)
Gene constraint: LOEUF 0.143 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.30
Residue 362: the 'disordered' region

Full SETBP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability, autosomal dominant 29 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Non-specific syndromic intellectual disability (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Childhood, Infancy

Similar variants

SETBP1 p.Glu16fs Pathogenic ★★ same condition
SETBP1 p.Ala1245fs Pathogenic ★ same condition
SETBP1 p.Glu697fs Pathogenic ★ same condition
SETBP1 p.Pro563fs Likely pathogenic ★ same condition
SETBP1 c.(540+1_541-1 Uncertain significance ★ same condition
SETBP1 p.Arg530Ter Pathogenic ★★ same condition
SETBP1 p.Arg544Ter Pathogenic/Likely pathogenic ★★ same condition
SETBP1 p.Arg589Ter Pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/setbp1-p-phe362fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown